Comment[ArrayExpressAccession]	E-GEOD-44958
MAGE-TAB Version	1.1												
Public Release Date	2013-07-03
Investigation Title	Smchd1 regulates autosomal genes subject to monoallelic expression												
Comment[Submitted Name]	Smchd1 regulates autosomal genes subject to monoallelic expression
Experiment Description	Analysis of the genes that escape silencing in the MommeD1 allele of Smchd1 Total RNA from E9.5 embryos compared in a two factor design - gender and Smchd1 genotype												
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl											
Person Last Name	Wakefield	Mould	Pang	Pakusch	Tonks	Stark	Carrie	Seidel	Ellis	Wakefield	Krause	Blewitt	Kay
Person First Name	Matthew	Arne	Zhenyi	Miha	Ian	Mitchell	Dianne	Annica	Jonathan	Matthew	Lutz	Marnie	Graham
Person Mid Initials	J	W			D				J	J		E	F
Person Email	wakefield@wehi.edu.au												
Person Affiliation	Walter and Eliza Hall Institute												
Person Address	Bioinformatics, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, Australia												
Person Roles	submitter												
Protocol Name	P-GSE44958-1	P-GSE44958-3	P-GSE44958-4	P-GSE44958-2	P-GSE44958-5								
Protocol Description	Data was processed using R2.11.1, beadarray 1.16.0.  Differential expression was analysed with limma using design matrix design=cbind(M.WT=c(1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0), M.MD=c(0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0), F.WT=c(0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0), F.MD=c(0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1), Array2=c(0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1)) ID_REF =  VALUE = quantile normalized Detection Pval = 	biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit from Applied Biosystems	Standard Illumina hybridization protocol	RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control (RIN>8) was performed with Agilent Bioanalyser.	Standard Illumina scanning protocol								
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol								
Experimental Factor Name	GENOTYPE	IMMUNOPRECIPITATE	SEX										
Experimental Factor Type	genotype	immunoprecipitate	sex										
Comment[SecondaryAccession]	GSE44958												
Comment[GEOReleaseDate]	2013-07-03												
Comment[ArrayExpressSubmissionDate]	2013-03-07												
Comment[GEOLastUpdateDate]	2013-07-03												
Comment[AEExperimentType]	transcription profiling by array												
Comment[AdditionalFile:Data1]	GSE44958_non-normalized.txt												
SDRF File	E-GEOD-44958.sdrf.txt